Proposal

To study the molecular basis for genetically ñ linked human birth defects.

The lab I intend to work in is at the Childrenís Hospital of Philadelphia and is headed by a clinical geneticist, Dr Ian Krantz. The goal of my summer internship is to study the molecular basis for genetically ñ linked human birth defects. Of particular interest are developmental disorders caused by mutation of regulatory genes. The identification of these genes and understanding how the mutation of one or more of these genes can affect many bodily systems is the all-important first step in providing care to the patients at the hospital. Traditional approaches such as chromosomal rearrangements and linkage analysis as well as less conventional ones are used to map these genes of interest. This will lead to a better understanding of the molecular basis of human embryonic development and the defects therein. Several developmental disorders are being studied in this context, including Cornelia de Lange syndrome, hearing loss, Alagille syndrome and congenital heart defects. Over the course of ten weeks during this summer I will be working closely with medical students, post doctoral students and other undergraduates on many of these projects and attending seminars on other researchersí work at the Childrenís Hospital and at the University of Pennsylvania.

Summary

Candidate genes for non-syndromic congenital hearing loss

This summer I worked in a genetics lab that studies the molecular basis of genetically-linked human developmental disorders. Research has been conducted on Alagille Syndrome, Cornelia de Lange syndrome, hearing loss and congenital heart defects. For a great deal of the summer I focused on the identification of novel genes for hearing loss. Hearing loss is interesting in that many genes have been implicated in the disorder and as many as 70% of hearing loss cases seem to have a genetic cause. The project focused on non-syndromic hearing loss, which has no other symptoms or structural defects associated with the hearing loss. The etiology of non-syndromic hearing loss is not well characterized, but it is a highly genetically heterogeneous diagnosis with approximately 100 genetic loci implicated. Identification of small genomic rearrangements using new technology would help in identifying causative genes and new loci for hearing loss.

The first step in this project was genome-wide SNP genotyping of over 600 bilateral sensorineural hearing loss probands. Copy number variations, deletions and duplications in the genome, were called by an algorithm which lists all of the copy number variations (CNVs) in a useable format. We use another computer-based algorithm developed in our lab to screen through these lists and to rank the CNVs based on their likelihood to be pathogenic. New techniques allow us to see smaller changes in the genome than before, which is very important for our purposes. After researching the genes involved in the highest ranked CNVs a few candidates are selected for sequencing. We chose PCDH20, a protocadherin precursor thought to be involved in calcium-dependent cell adhesions in the brain; SLC2A4RG, which regulates GLUT4; and CRISPLD2. All of the CNVs involved deletions in exonic regions, were relatively small and were not covered by literature or in-house controls. As of this writing, sequencing for these genes has not been completed. At least two potentially deleterious changes were found, one in PCDH20 (117C>A, S39R) and one in SLC2A4RG (365G>A, G122E). Further characterization needs to be done before validating these changes.

Future work will focus more on regulatory elements lying outside of the coding regions. Changes in these regulatory elements are more likely to be implicated in many non-syndromic hearing loss cases than large exonic changes. Large changes in coding regions can affect gene expression in many cell types throughout the body, whereas changes in regulatory elements affect only the genes they regulate. These changes are more specific and may account for many cases of isolated hearing loss. Changes to the scoring parameters of our CNV ranking program must be made in order to identify and accordingly score these important regions. The next project will focus on using this approach with samples from patients with congenital heart defects.

Poster (saved as a pdf)